For me the Justice/Grissom trade was the most confusing, mainly the timing. I was irrate at that time and up to that point JS was great as GM of the Braves, but after that point going forward he made some questionable moves, especially in the late 90s with what he didn't do and with what he did do in the next decade. And he executed another head scratcher a few days later trading Dye. It's like JS didn't have a plan and just wanted to make a splash before the opening of Turner Field.
But nothing compares to the Millwood fiasco. I've never been so irrate in my life, primarily because it was a transition period for the braves, but JS pigeonholed himself into having to make that trade by acquiring mediocre pitching in Ortiz, Byrd, and Hampton. I was in college at that time in sport management and after that I decided no more for me and didn't pursue it any further. JS also solidified himself as overrated and living on reputation from his first half of his tenure here. The only thing about the "economics of baseball stink" is that the planning and execution of JS more than "stinker like dead road kill."
A distant third is Javier Vazquez. I always dreamed of being able to pitch for us and realize his potential and be great, and that he was for his one season here....he was dominant only for Wren to dump him for Melky freakin Cabera and Vizcaino. Never have and did understand the FOs boner for Melky, they tried to acquire him for years.